Actually the reason Amtrak runs a huge deficit is their long haul routes (cross country). Their local routes like the eastern corridor and even the ones on the west coast are profitable. Even their regional routes either break even or are very close.

I would point you to the following Wendover Productions video that gives a great analysis.

Amtrak’s Grand Plan for Profitability

https://www.youtube.com/watch?v=dSw7fWCrDk0